Save Me
by shadowsinthesunshine
Summary: Clary is taken from The Institute, but who would take her? How will Jace and the others find her, and who will she be when they do? Who is this new group against the Shadowhunters? And why do they want Clary? Clary/Jace, Izzy/Simon, Magnus/Alec *May include self harm*
1. Taken

Isabelle yanked Clary's hair into a high ponytail, only to drop it back down to her shoulders.  
"Clary, we have got to so something with this hair," she said, an annoyed looked on her face.  
Clary smirked.  
"Izzy, I'll handle the hair, you worry about the fashion."  
This lit up Isabelle's face, and with a bright smile, she skipped off to the closet.  
"Izzy, clothes! Not something that no one should wear in private, let alone in public!"  
Isabelle laughed, "Have a little faith, Clary! You're gonna look fabulous!"  
Clary rolled her eyes. Though they had a rough beginning, Isabelle had grown into a sister. She would do anything for the girl, which she often proved in their fights with demons.  
A loud knock pounded on the room's door.  
"I've got it Izzy!"  
Clary checked in the mirror to make sure she looked presentable, just in case it was Jace.  
She walked over to the door as another loud knock sounded. "I'm coming," she yelled.  
She happily opened the door, flashing one of her trademark grins.  
A sharp pain flew through her stomach. She looked down. A dagger was shoved deep into her abdomen.  
Shocked, she slowly looked up. Her vision was beginning to blur, and she fell against the door frame.  
A blurred figure stood over her. She heard a small chuckle.  
"W-who are you?"  
"Clary, dear, you'll find out soon enough," a deep voice said.  
Clary slowly moved her hand to the dagger, using all her strength to attempt pulling it out. She had pulled it halfway out when her hand was ripped away.  
"Ah ah ah Clary. I plan to put you through as much pain as possible during our short time together. Well, short for you anyways."  
He chuckled and pushed the dagger back down.  
Clary started to scream, but the sound was muffled by the man's gloved hand.  
He lifted her whimpering body off the ground.  
Clary saw as he pulled an object out of his pocket, and drew a portal.  
She heard Jace and Alec's laughing voices coming around the corner.  
"J-jace," she struggled to yell out.  
"Clary?"  
"Clary! Put her down! Wait, Clary!"  
She heard their running footsteps as she felt the darkness of pain pull at her.  
The man stepped through the portal.  
Then all went black.

Reviews? Ideas? Thoughts? Hope ya liked! :)


	2. Surprise

**Hey guys! Wow, I was so surprised and pleased on the feedback of this story, even in just the first hour! I appreciate it so much, and it really helped me to improve the story. I got some reviews about formatting, the first chapter was typed on my phone, so it was really hard to format it correctly, but this one is from a laptop! I also got reviews on when this story takes place, so to clear that up, I honestly didn't even have a set time period in mind when I wrote it. I haven't read the 5th book completely yet, but I doubt this story will include much about Sebastian (Jonathan) or Valentine, so anytime between the 1st and 3rd books will work. I'm glad you guys are wondering who kidnapped Clary! If you have any questions, review or PM me! Please review! Enjoy!**

**Jace POV**

I paced around the floor of the institute, waiting for someone to tell me this whole thing is a joke, to see Clary run from the large door into his arms.

He knew it wasn't.

He could hear Isabelle crying softly from the corner. He glanced over at her, surprised by the blotchy, red-faced girl he saw.

"Isabelle," he leaned down to her, "Izzy, it isn't your fault. You couldn't have known, just like Alec and I didn't know."

She looked up at me, her face showing worry, shame, destruction.

"It is my fault Jace. I was right there, I was there the whole time. I was just being stupid, worrying about clothes she didn't even want to wear. I was looking at stupid clothes while Clary was being taken! Dammit Jace, don't you dare tell me this isn't my fault!"

I pushed a piece of hair behind her ear and let her fall onto me, her tears soaking my shirt. No matter how much I tried to comfort her, we both knew it was true. While it wasn't her fault, she was there, whip distance away, a distance that could have saved Clary.

The door of the room swung open, causing Jace to jerk his head towards it. His heart fluttered, hoping to the angel that it was Clary. To his dismay, only an upset Alec and Magnus quickly walked in.

"Well blondie, don't look so excited to see me," Magnus said with a wink. I don't see how he can joke right now, when Clary could be in danger.  
Magnus must have realized what I was thinking, because he looked me in the eye and said, "I love that feisty redhead too, Jace. And I'm going to do all that is within my ability to get her back to us." I looked up at him and smiled, or at least as much of a smile I could muster up.

"Now, could you guys tell me exactly what you saw when the man stepped through with Clary?" Magnus questioned.

When I remained silent, Alec spoke, "He was dressed all in black, with a hood and gloves, and she-"

"You know, this would be much faster if I just do this," Magnus interrupted. He muttered a few words, grabbed Alec's hand, then brought it up to his forehead. After a few moments, he slowly opened his eyes and brought it down.

"The man, he was one of you, a Shadowhunter."

**Clary POV**

I slowly drifted out of my sleep, blinking away the blur that I saw in front of me. My head is pounding, but when I try to reach my hand up to my forehead, I discover that they are tied down. I jerk them, but I can't seem to free them from the restraints.

"Stop trying to fight it, Clary," I heard a voice say. I moved my head towards it. I saw a boy, seemingly close to my age, hunched over a table.

"W-who are you?" I asked, trying to find my voice. He turned, and I saw that his face was covered with a mask. He was carrying a tray, with what looked to be medical supplies. He unlocked the chains on my hands, and I instantly shot up, prepared to escape. I was stopped by the searing pain that formed in my abdomen, which I vaguely remembered had been daggered.

The boy eased me back down onto the bed. "Just stay calm Clary, I'm going to change your bandages."

"Why don't you just use a healing rune?" the words slipped from my mouth. He stopped with the bandaging, glancing over at me, then he looked back down. "Runes won't work here," he said quietly. "Your wounds won't heal by the time you leave here, but I will make sure a rune gets placed on you once you're out of this place."

_Runes won't work_, she thought. _Why wouldn't they work?_

As if reading her mind, the boy said, "There is a spell set on this place, by one of the warlocks, nothing like that can be used. It's hell for the Shadowhunters," he said with a chuckle, "but I don't much mind it."

She gasped. "You're.. a Shadowhunter?" Why would a Shadowhunter be here? And if he wasn't the one who took her from the Institute, were there more?

**Woot you made it to the end! Hope ya liked! Who is this mystery guy? Please review!**


	3. Hurt

**Hey guys! :) Hope you're enjoying so far! As to the reviews asking if the mystery man is hot, he's stunning! I will try and come up with a picture and post it to my profile! :) Enjoy this chapter and please send me things you'd like to see! :)**

**CAUTION- this chapter contains some vivid scenes. If they make you uncomfortable, I apologize. You can skip to the end and gather the info needed :) **

**Clary POV **

I awoke from my exhaustion induced sleep at the sound of a slamming door. A man walked in, fully clothed with a mask.

"Hello dear Clary." That voice. It seems so familiar.

"Now," he began, "if you haven't figured it out yet, I am the one who kidnapped you, as the mundanes say," he chuckled.

"Why did you take me? I'm of no use in some place of evil!" He turned his head sharply to me.

"I'm so tired of hearing you talk, dear," he said, while retrieving a roll of what looked to be duct tape. He tore a piece off, then spread it over my mouth. My breath caught.

He then leaned over me, placing his hand on my side, then rubbing them down my legs. My screams for help were muffled by the tape over my mouth. He proceeded to raise my shirt, revealing my bra. He began to inspect my wound, but it was clear he wanted to inspect other things as well. Why was he doing this?

He pressed down on my wound, causing me to wince in pain. He looked over at me, a smile spreading on his face. "Did I not tell you my intentions of putting you through as much pain as I can in your stay?" With each word he pressed down harder on my stomach. He walked over to the table, and grabbed the medical supplies the boy had used. My eyes widened as he put rubbing alcohol onto the tray, along with a knife.

"No, no please," my muffled voce sounded through the tape. He grinned, pulling off my bandage, revealing the large stab wound. With a look of pride on his face, he opened the bottle of alcohol. I again begged for him to stop, but he acted as though he couldn't hear me.

Just then, the door swung open, revealing the boy. The man glanced up I'm surprise. "Ah James, nice of you to join us." The boy, James, looked wide eyes at the bottle. He moved over towards the man, attempting to grab the bottle, but resulting in it accidentally being dropped onto me.

The clear liquid poured onto me, burning in my wound. I screamed, audible even through the tape. James jumped towards me, throwing the bottle, and grabbing a towel, which he pressed firmly against my skin.

"You always were too caring James," the man said.

James looked up at him.

"I hate you, father."

**oooh a twist! Hope ya liked! Sorry this chapter was a bit vivid, I just wanted some action :) please review! **


	4. You Found Me

**I barely got any reviews on the previous chapter :( but that's okay! :)**

**IMPORTANT- I posted pics on my profile of what I imagine James looks like! Hope you pictured him the same way! :)**

**James POV**

I stood in the corner of the room, my eyes lying on Clary's sleeping body. She looked so peaceful, a look I hadn't seen from her since she had arrived here. She always looked so happy when she was with that blonde boy. I turned quietly, attempting to not wake the finally calm girl, and walked towards the door.

"James?" I heard a mumble. I turned toward the voice, seeing Clary beginning to wake. "Yes?" I asked her.

"That was your dad? The one who took me? Why is he doing this?"

I looked to the dirty, tile floor. This was a question I had often asked myself since I was just a kid. Why was my father such a monster? "It's his job Clary, it's just his job," I replied, silently begging her not to ask anything else.

"And your mom?" she asked. I squeezed my eyes shut, willing the tears to go away. I stood silent for a moment, searching for an answer. "She's.. dead."

I saw the look of sympathy on her face. I didn't want that. I walked over to her.

"Clary, if I'm caught telling you this, it's possible they will kill me, but you have the right to know where you are," she looked eagerly into my eyes. This was the first time someone truly looked into my eyes.

"This is, well, a secret society I guess you could call it. It's members include rogue Warlocks, Shadowhunters, Werewolves, Vampires, the whole deal. All people who are against the norm. My father just happens to be the lead. He always had a little crazy streak in him, but I never thought he would be capable of this. This 'society' usually keeps to itself, they don't generally even associate themselves with all of you. It's always been just talk. Just sitting around the conference table discussing all the terrible plans they've came up with. No actions have ever been taken. I hear bits and pieces of it, because I have to serve them during the meetings, but I stood by the door and listened when they discussed their plan for you."

"Clary, they know how powerful you are. How much you can benefit and improve their enemies. They.. they want to rid you of your powers, of your skills. And if they can't do that they'll use you against your friends. Or they plan to kill you. God, Clary, I am so sorry. But there is nothing I can do. Anyone who tries to rebel against the society pays with their life. The only reason I haven't is because of my dad. But I don't have many chances left."

I got up from beside her and combed my hair back with my fingers.

"I'll get you out of here Clary. I won't let them hurt you, I won't let what happened to my mom happen to you. I don't know how, and I don't know when, but I will get you out. You have to trust me. I will try and keep them from hurting you as much as I can, but there's only so much I can do."

I turned and walked towards the door.

"What happened to her? Your mom," she asked.

I looked up at the door. Grabbing the knob I said, "He killed her." Then I walked out.

I walked down the blinding, white hallway towards my room. I fell down onto my bed, tears soaking my eyes. I pulled out my phone, turning on some music.

_"Lost and insecure, you found me, you found me. Lying on the floor, surround me. Why'd you have to wait. Where were you?"_

**How'd you guys like James POV? I hope you loved this chapter, I tried so hard on writing this! :) Please review, it really encourages me to update! :)**


	5. Escape

**Clary POV**

"Clary, stop moving!"

I screamed and struggled on the table as Jame's dad brought a needle down towards my arm. I didn't know what it was, what it would do, and I wasn't planning to find out.

"James! James, please stop him! Help me!" I spat out.

A sudden beating came upon the door. "Clary! Father, what are you doing?! Let me in!" He continued to beat on the door.

I felt a sharp stab in my arm, and the thick liquid being inserted into my veins. Tears dripped down my cheeks, falling onto the table. My vision blurred and I began coughing. My breathing quickened, my lungs felt like they had shrunk to the size of a pebble. Jame's father leaned down to me.

"Clary, these are your orders."

**James POV**

I busted through the door, running over to Clary. She lay unconscious, tears staining her beautiful, pure face.

I looked to my father, "What the hell did you do to her?!"

He chuckled, a vicious smile spreading upon his face. I punched him in the jaw, bringing blood from his mouth. He laughed and turned toward the door.

"Try and save her now," he told me, then he walked out of the door. I ran towards Clary.

"Oh my God. I'm so sorry. I cut the ties around her hands, feet, and stomach, and pulled her towards me, burying my face in her hair. I could feel my tears wetting her hair.

I pulled out my blade, squeezed my eyes, preparing for the pain, and drew a portal. Grabbing Clary's too-light body, I stepped through. We were thrown into the alley behind the Institute.

Blade in my hand I drew a rune on myself to dull the pain of going against the spell set on the Society's building. The fire in my body calmed to a dull heat, and I let out a breath.

I heard a soft groan coming from Clary. Jolted back into the present, I used my blade to draw healing runes onto her. Her eyes slowly opened, revealing the beautiful emerald green I had grown to love.

"James? Where are we? How did you get me out? What did he do-"

"Shh Clary," I tried to calm her, but honestly I was changing the subject because I didn't know what they had done. It was never discussed in the meetings, I never read it in their minds.

I stood up, lifting Clary up to her feet. She noticed her surroundings, gasping at the sight of the Institute. Tears sprung to her eyes. She stepped towards it, stopped, then turned back to me.

"Go," I told her, sending and encouraging smile.

She smiled back at me and ran towards the Institute.

Then the pain began. I had been out for too long.

**Jace POV**

I slid down the wall in the entrance way, tears sliding down my cheeks.

_What am I doing, _I thought, _I'm Jace. I don't cry._

But that didn't stop the tears. I missed Clary, and though no one would admit it, we were all imagining the worst.

That's when the door opened. My hand shot to my blade, preparing to attack, but what I saw caused my heart to leap from my chest.

"Clary!" I yelled.

**Two chapters in one night! I might even add another.. I have school starting back on Monday, so I'm trying to update as much as I can! :) Pleaseeee Review!**


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